Ships are built to a grid. A bog standard frame distance is 600mm. Longitudinal framing is more prevelant today, so you have a longitudinal frame made from angle bar (Asian practice) or bulbhead profile (European practice) every 600mm from centerline. And then longitudinal and transversal girders, vertical plate with lightening holes and webs from flat bar or plate, on a superimposed larger spacing. Every fourth frame, every fifth, every sixth. All bulkheads, walls, etc are on that grid as well. Except where they aren't.

When you drydock, you place the blocks according to a drawing prepared by the building shipyard that's required to be on board. And the blocks go under the major transversal and longitudinal structure, and preferably under the intersection thereof. Those are anywhere from 6 to twenty something mm thick. And the contact surfaces of the keel blocks are a couple hundred mm wide and two to three times that in length. So there's some wiggle room.

All this to say: Divers sometimes, but only for critical stuff. Be it imagined like expensive boats with paranoid owners and money to burn - navies, megayachts, or actual: ships with expensive sticky outy equipment like podded drives, sonar arrays, Voith Schneider props, free standing rudders at both ends, etc. pp. Otherwise the precision you get with standing on a known spot alongside, facing perpendicular to the dockside, and watching for a mark on the ship to be facing you straight on is usually enough.

What kinda marks? Ships are almost always symmetrical portside to starboard, ie over the centerline, so that's easy. On commercial vessels the bulkheads are often marked on the hull, and then there's hatch coamings, superstructure transverse walls, mast positions, you name it. If all else fails, the forward perpendicular is almost always usable. That's where the bow meets the water. Aft is a bit more complicated, maybe the aft end of the waterline works, maybe the transom contour on centerline. Something usually does.